void Motif::read(istream& motin) {
char line[200];
vector<int> c;
vector<int> p;
vector<bool> s;
// Read sites
// (don't add yet, as they will get screwed up by the column changes)
while(motin.getline(line, 200)) {
if(line[0] == '*') break;
strtok(line, "\t");
c.push_back(atoi(strtok(NULL, "\t")));
p.push_back(atoi(strtok(NULL, "\t")));
s.push_back(atoi(strtok(NULL, "\0")));
}
int motwidth = strlen(line);
columns.clear();
for(int i = 0; i < motwidth; i++) {
if(line[i] == '*') add_col(i);
}
// Add sites
sitelist.clear();
int num_sites = c.size();
for(int i = 0; i < num_sites; i++) {
assert(p[i] >= 0);
add_site(c[i], p[i], s[i]);
}
// Read MAP score
motin.getline(line, 200);
strtok(line, ":");
set_map(atof(strtok(NULL, "\0")));
// Read specificity
motin.getline(line, 200);
strtok(line, ":");
set_spec(atof(strtok(NULL, "\0")));
// Read sequence cutoff
motin.getline(line, 200);
strtok(line, ":");
set_seq_cutoff(atof(strtok(NULL, "\0")));
// Read expression cutoff
motin.getline(line, 200);
strtok(line, ":");
set_expr_cutoff(atof(strtok(NULL, "\0")));
// Read iteration found
motin.getline(line, 200);
strtok(line, ":");
set_iter(strtok(NULL, "\0"));
// Read dejavu
motin.getline(line, 200);
strtok(line, ":");
set_dejavu(atoi(strtok(NULL, "\0")));
}
int
Task_Entry::reframe (ACE_Unbounded_Set <Dispatch_Entry *> &dispatch_entries,
Task_Entry &owner,
ACE_Ordered_MultiSet <Dispatch_Entry_Link> &set,
u_long &set_period, u_long new_period)
{
int result = 0;
// if the set period is zero, treat it as uninitialized,
// and simply value the set period with the new period
if (set_period)
{
// make sure the new period is greater than the current
// set period, and that they are harmonically related
if (new_period <= set_period)
// return an error if they're not harmonically related,
// do nothing if set's frame is a multiple of the new frame
return (set_period % new_period) ? -1 : 0;
else if (new_period % set_period)
return -1;
// make a shallow copy of the set in a new ordered multiset
// using the Dispatch_Entry_Link smart pointers
ACE_Ordered_MultiSet <Dispatch_Entry_Link> new_set;
ACE_Ordered_MultiSet_Iterator <Dispatch_Entry_Link> new_iter (new_set);
ACE_Ordered_MultiSet_Iterator <Dispatch_Entry_Link> set_iter (set);
for (set_iter.first (); set_iter.done () == 0; set_iter.advance ())
{
Dispatch_Entry_Link *link;
if (set_iter.next (link) == 0)
return -1;
else if (new_set.insert (*link, new_iter) < 0)
return -1;
}
// Do a deep copy merge back into the set using the new period
// and starting after the 0th sub-frame: this puts all
// dispatches after the 0th sub-frame of the new period into the
// set, and leaves existing dispatches in the 0th sub-frame of
// the new period in the set as well.
result = merge_frames (dispatch_entries,
owner,
set,
new_set,
new_period,
set_period,
1,
1);
}
// update the set's period to be the new frame
set_period = new_period;
return result;
}
static int _fetch_string_values( struct strset *s, const char **out, int max ) {
void *cookie;
const char *v;
int n = 0;
if( set_iter( s, &cookie ) ) {
while( n < max && set_next( s, &cookie, &v ) ) {
if( _isalpha( v ) ) {
out[ n++ ] = v;
}
}
}
return n;
}
